Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 48 of 66
Found at i:17250150 original size:25 final size:25
Alignment explanation
Indices: 17250110--17250168 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
17250100 TTATTATTTC
* ** *
17250110 AAAACTATTCTTATTAATTAAATATT
1 AAAA-TATTCCTATTAACCAAACATT
17250136 AAAATATTCCTATTAACCAAACATT
1 AAAATATTCCTATTAACCAAACATT
17250161 AAAATATT
1 AAAATATT
17250169 ACGAGAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAATATTCCTATTAACCAAACATT
Found at i:17254464 original size:26 final size:26
Alignment explanation
Indices: 17254430--17254486 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
17254420 GAATTAAACA
* * * *
17254430 TTTTAAATATTATATGTAATAATATT
1 TTTTTAATATAATATATAAAAATATT
17254456 TTTTTAATATAATATATAAAAATATT
1 TTTTTAATATAATATATAAAAATATT
17254482 TTTTT
1 TTTTT
17254487 TAACATGACG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTTTAATATAATATATAAAAATATT
Found at i:17254509 original size:26 final size:26
Alignment explanation
Indices: 17254446--17254511 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
17254436 ATATTATATG
* * *
17254446 TAATAATATTTTTTTAATATAATATA
1 TAATAATTTTTTTTTAACATAACATA
* * *
17254472 TAAAAATATTTTTTTTAACATGACGTA
1 TAATAAT-TTTTTTTTAACATAACATA
17254499 TAATAATTTTTTT
1 TAATAATTTTTTT
17254512 ATGAGTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
26 12 0.38
27 20 0.62
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (26 bp):
TAATAATTTTTTTTTAACATAACATA
Found at i:17264266 original size:24 final size:24
Alignment explanation
Indices: 17264196--17264313 Score: 116
Period size: 24 Copynumber: 5.0 Consensus size: 24
17264186 GATTAAATTA
*
17264196 TTACACGTCATGTATAAAAACATG
1 TTACACGTAATGTATAAAAACATG
* * * * **
17264220 TGACATGTTATG-AT--TAAGTTG
1 TTACACGTAATGTATAAAAACATG
*
17264241 TTACACGCAATGTATAAAAACATG
1 TTACACGTAATGTATAAAAACATG
*
17264265 TTACACGTAATGTACAAAAACATG
1 TTACACGTAATGTATAAAAACATG
* *
17264289 TCACACGTAATGTATAAAAATATG
1 TTACACGTAATGTATAAAAACATG
17264313 T
1 T
17264314 GATATGTCAT
Statistics
Matches: 73, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
21 12 0.16
22 2 0.03
23 2 0.03
24 57 0.78
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (24 bp):
TTACACGTAATGTATAAAAACATG
Found at i:17264307 original size:48 final size:48
Alignment explanation
Indices: 17264243--17264344 Score: 132
Period size: 48 Copynumber: 2.1 Consensus size: 48
17264233 TTAAGTTGTT
*
17264243 ACACGCAATGTATAAAAACATGTTACACGTAATGTACAAAAACATGTC
1 ACACGCAATGTATAAAAACATGTGACACGTAATGTACAAAAACATGTC
* * * * * * *
17264291 ACACGTAATGTATAAAAATATGTGATATGTCATGTACAAAAATATGTG
1 ACACGCAATGTATAAAAACATGTGACACGTAATGTACAAAAACATGTC
17264339 ACACGC
1 ACACGC
17264345 CATGGTTAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (48 bp):
ACACGCAATGTATAAAAACATGTGACACGTAATGTACAAAAACATGTC
Found at i:17264348 original size:24 final size:24
Alignment explanation
Indices: 17264243--17264343 Score: 112
Period size: 24 Copynumber: 4.2 Consensus size: 24
17264233 TTAAGTTGTT
* * *
17264243 ACACGCAATGTATAAAAACATGTT
1 ACACGTAATGTACAAAAACATGTG
*
17264267 ACACGTAATGTACAAAAACATGTC
1 ACACGTAATGTACAAAAACATGTG
* *
17264291 ACACGTAATGTATAAAAATATGTG
1 ACACGTAATGTACAAAAACATGTG
* * * *
17264315 ATATGTCATGTACAAAAATATGTG
1 ACACGTAATGTACAAAAACATGTG
17264339 ACACG
1 ACACG
17264344 CCATGGTTAG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.26
Consensus pattern (24 bp):
ACACGTAATGTACAAAAACATGTG
Found at i:17264383 original size:45 final size:45
Alignment explanation
Indices: 17264321--17264407 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
17264311 TGTGATATGT
* **
17264321 CATGTACAAAAATATGTGACACGCCATGGTTAGGTTGTTACACAC
1 CATGTACAAAAACATGTGACACAACATGGTTAGGTTGTTACACAC
*
17264366 CATGTACAAAAACATGTGACACAATATGGTTAGGTTGTTACA
1 CATGTACAAAAACATGTGACACAACATGGTTAGGTTGTTACA
17264408 TGTCATATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (45 bp):
CATGTACAAAAACATGTGACACAACATGGTTAGGTTGTTACACAC
Found at i:17265287 original size:31 final size:31
Alignment explanation
Indices: 17265249--17265322 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
17265239 ACATTCAATC
* * *
17265249 AAATTTTTATTTTTTTTATTTTTAGTGAAAT
1 AAATTTTTATTTTTTCTATTTTGAGTCAAAT
*
17265280 AAATTTTTATATTTTCTATTTTGAGTCAAAT
1 AAATTTTTATTTTTTCTATTTTGAGTCAAAT
*
17265311 AAGTTTTTATTT
1 AAATTTTTATTT
17265323 AATAATTGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.61
Consensus pattern (31 bp):
AAATTTTTATTTTTTCTATTTTGAGTCAAAT
Found at i:17265846 original size:41 final size:40
Alignment explanation
Indices: 17265780--17265856 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 40
17265770 TATAACATAA
17265780 CAAGAGAGGCTAGGCTTTGGAAAAAAACAGAGAGATTAGAG
1 CAAGAGAGGCTAGGCTTTGGAAAAAAA-AGAGAGATTAGAG
*
17265821 CAAGGGAGGCTAGGCTTT-GAGAAAAAAAGAGAGATT
1 CAAGAGAGGCTAGGCTTTGGA-AAAAAAAGAGAGATT
17265857 TGAGAAGCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
40 11 0.32
41 23 0.68
ACGTcount: A:0.43, C:0.09, G:0.32, T:0.16
Consensus pattern (40 bp):
CAAGAGAGGCTAGGCTTTGGAAAAAAAAGAGAGATTAGAG
Found at i:17269488 original size:13 final size:13
Alignment explanation
Indices: 17269470--17269494 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17269460 TTCCAGAAAA
17269470 TTTATAAAATCAT
1 TTTATAAAATCAT
17269483 TTTATAAAATCA
1 TTTATAAAATCA
17269495 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:17275068 original size:5 final size:5
Alignment explanation
Indices: 17275060--17275094 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
17275050 CAATCGAACC
*
17275060 TAACT TAACT TAACT TAACT TATCT TAACT TAACT
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT
17275095 GGACTTGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (5 bp):
TAACT
Found at i:17280925 original size:51 final size:51
Alignment explanation
Indices: 17280849--17281002 Score: 299
Period size: 51 Copynumber: 3.0 Consensus size: 51
17280839 AGACTTAGGT
17280849 AGATTACCCAAGATCAAAACACTTATCACCACTCATTGACAAAAATTAAAC
1 AGATTACCCAAGATCAAAACACTTATCACCACTCATTGACAAAAATTAAAC
*
17280900 AGATTACCTAAGATCAAAACACTTATCACCACTCATTGACAAAAATTAAAC
1 AGATTACCCAAGATCAAAACACTTATCACCACTCATTGACAAAAATTAAAC
17280951 AGATTACCCAAGATCAAAACACTTATCACCACTCATTGACAAAAATTAAAC
1 AGATTACCCAAGATCAAAACACTTATCACCACTCATTGACAAAAATTAAAC
17281002 A
1 A
17281003 TACTTTCCTA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 101 1.00
ACGTcount: A:0.47, C:0.25, G:0.06, T:0.22
Consensus pattern (51 bp):
AGATTACCCAAGATCAAAACACTTATCACCACTCATTGACAAAAATTAAAC
Found at i:17290445 original size:16 final size:15
Alignment explanation
Indices: 17290426--17290468 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
17290416 TTATTTATTT
17290426 TTAGTTATTTTTATAA
1 TTAGTTATTTTTA-AA
*
17290442 TTAGTTTATTTTTAAG
1 TTAG-TTATTTTTAAA
*
17290458 TGAGTTATTTT
1 TTAGTTATTTT
17290469 AATTTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 8 0.33
17 9 0.38
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (15 bp):
TTAGTTATTTTTAAA
Found at i:17293503 original size:38 final size:40
Alignment explanation
Indices: 17293453--17293558 Score: 126
Period size: 38 Copynumber: 2.7 Consensus size: 40
17293443 ATAGTGCCTG
* *
17293453 TGTGCACGATGTGGGGGGATGTACATGATGACACT-AAT-
1 TGTGCACAATGTGGGGGGATGCACATGATGACACTGAATA
** * **
17293491 TGTGCACAATGTGGGGGGATGCACGCGATGGCACTGGCTA
1 TGTGCACAATGTGGGGGGATGCACATGATGACACTGAATA
*
17293531 TGTGCACTATGTGGGGGGATGCACATGA
1 TGTGCACAATGTGGGGGGATGCACATGA
17293559 GCCGGGTGTG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 30 0.54
39 1 0.02
40 25 0.45
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.24
Consensus pattern (40 bp):
TGTGCACAATGTGGGGGGATGCACATGATGACACTGAATA
Found at i:17296092 original size:31 final size:28
Alignment explanation
Indices: 17296026--17296133 Score: 119
Period size: 28 Copynumber: 3.8 Consensus size: 28
17296016 CTTTTTCATA
*
17296026 TTTGTCTTAATTTAGACAAGAAAACATG
1 TTTGTCTTAATTTAAACAAGAAAACATG
*
17296054 TTTGTCTTAATTTAAAACAAGAAAAATATG
1 TTTGTCTTAATTT-AAACAAG-AAAACATG
** *
17296084 TTTTGTCTTAATTTGGATAAGAAAACAT-
1 -TTTGTCTTAATTTAAACAAGAAAACATG
*
17296112 ATTGATCTTAATTTAAACAAGA
1 TTTG-TCTTAATTTAAACAAGA
17296134 TAACTTGTGT
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
27 3 0.05
28 27 0.41
29 12 0.18
30 11 0.17
31 13 0.20
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (28 bp):
TTTGTCTTAATTTAAACAAGAAAACATG
Found at i:17309856 original size:29 final size:29
Alignment explanation
Indices: 17309728--17310060 Score: 376
Period size: 28 Copynumber: 11.7 Consensus size: 29
17309718 TCTTTTCTTT
***
17309728 AATTAAGACAAAACATGTTAAGTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
* *
17309757 AATTGAGAC-AAATATGTTTTCTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
* * *
17309785 GATTAAGACAAAACATATTTT-TGCTATCTTA
1 AATTAAGACAAAACATGTTTTCT--TGTC-TA
*
17309816 AATTAAGACAAAACATGTTTTCTTATCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
*
17309845 AATTAAGAC-AAACATGCTTTCTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
** *
17309873 AATTAAGACAAAA-AAATTTTCTTGTCTC
1 AATTAAGACAAAACATGTTTTCTTGTCTA
*
17309901 AATTAAGACAAAATATGTTTTCTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
* *
17309930 AACTAAGAC-AAACATGTTTTCCTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
* * ** *
17309958 AACTAAGAC--AACATATTAACTTGTCCA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
*
17309985 AATTAAGACAAAATATGTTTTCTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
*
17310014 AATTAAGAC-AAACATGTTTTTTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
17310042 AATTAAGACAAAACATGTT
1 AATTAAGACAAAACATGTT
17310061 AAAGCTGTTT
Statistics
Matches: 257, Mismatches: 37, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
27 21 0.08
28 125 0.49
29 82 0.32
30 7 0.03
31 21 0.08
32 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (29 bp):
AATTAAGACAAAACATGTTTTCTTGTCTA
Found at i:17309923 original size:57 final size:57
Alignment explanation
Indices: 17309728--17310060 Score: 370
Period size: 57 Copynumber: 5.8 Consensus size: 57
17309718 TCTTTTCTTT
*** * *
17309728 AATTAAGACAAAACATGTTAAGTTGTCTAAATTGAGACAAATATGTTTTCTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAAAATGTTTTCTTGTCTA
* * * *
17309785 GATTAAGACAAAACATATTTT-TGCTATCTTAAATTAAGACAAAACATGTTTTCTTATCTA
1 AATTAAGACAAAACATGTTTTCT--TGTC-TAAATTAAGACAAAA-ATGTTTTCTTGTCTA
* ** *
17309845 AATTAAGAC-AAACATGCTTTCTTGTCTAAATTAAGACAAAAAAATTTTCTTGTCTC
1 AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAAAATGTTTTCTTGTCTA
* * * *
17309901 AATTAAGACAAAATATGTTTTCTTGTCTAAACTAAGACAAACATGTTTTCCTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAAAATGTTTTCTTGTCTA
* * ** *
17309958 AACTAAGAC--AACATATTAACTTGTCCAAATTAAGACAAAATATGTTTTCTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAAA-ATGTTTTCTTGTCTA
*
17310014 AATTAAGAC-AAACATGTTTTTTTGTCTAAATTAAGACAAAACATGTT
1 AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAAA-ATGTT
17310061 AAAGCTGTTT
Statistics
Matches: 228, Mismatches: 40, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
55 24 0.11
56 43 0.19
57 110 0.48
58 6 0.03
59 22 0.10
60 23 0.10
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (57 bp):
AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAAAATGTTTTCTTGTCTA
Found at i:17318249 original size:22 final size:22
Alignment explanation
Indices: 17318221--17318264 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17318211 TTCTATTGGT
17318221 ATCAGAGCTTTTGGTTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
*
17318243 ATCAGAGTTTTTGGTTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
17318265 TGGTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (22 bp):
ATCAGAGCTTTTGGTTTTAAAG
Found at i:17332988 original size:43 final size:43
Alignment explanation
Indices: 17332940--17333096 Score: 219
Period size: 43 Copynumber: 3.7 Consensus size: 43
17332930 TTGACTCGGC
17332940 TATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGACCC-GAT
1 TATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGACCCAG-T
* *
17332983 TATGTGCGAGTAGGGAGTGCACATAA-CCCAGTGATGACCCAGT
1 TATGTGCGAGTAGGGAGTGCGCATAAGCCGA-TGATGACCCAGT
* * *
17333026 TATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGACCTAGC
1 TATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGACCCAGT
* *
17333069 CATGTGGGAGTAGGGAGTGCGCATAAGC
1 TATGTGCGAGTAGGGAGTGCGCATAAGC
17333097 TGGGAATGAT
Statistics
Matches: 102, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
42 3 0.03
43 95 0.93
44 4 0.04
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.20
Consensus pattern (43 bp):
TATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGACCCAGT
Found at i:17333138 original size:26 final size:26
Alignment explanation
Indices: 17333102--17333162 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
17333092 TAAGCTGGGA
17333102 ATGATGATGATGGGATGGTGTGCATG
1 ATGATGATGATGGGATGGTGTGCATG
17333128 ATGATGATGATGGGATGGTGTGCATG
1 ATGATGATGATGGGATGGTGTGCATG
17333154 ATGATGATG
1 ATGATGATG
17333163 GGTATATGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.31
Consensus pattern (26 bp):
ATGATGATGATGGGATGGTGTGCATG
Found at i:17333348 original size:21 final size:21
Alignment explanation
Indices: 17333305--17333348 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
17333295 TGTTCTGATC
* **
17333305 CTCGCTGTAGCGAGATTCATT
1 CTCGCTGCAGCGAGAAACATT
*
17333326 CTCGCTGCAGCGAGAAACTTT
1 CTCGCTGCAGCGAGAAACATT
17333347 CT
1 CT
17333349 GTCCATTTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (21 bp):
CTCGCTGCAGCGAGAAACATT
Found at i:17334685 original size:18 final size:18
Alignment explanation
Indices: 17334658--17334704 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
17334648 TCACGTTTGG
*
17334658 TGGGTGATCCACTTATGA
1 TGGGTTATCCACTTATGA
* *
17334676 TGGGTTATCCACTTTTGG
1 TGGGTTATCCACTTATGA
*
17334694 TGGATTATCCA
1 TGGGTTATCCA
17334705 TTTTTAGCGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (18 bp):
TGGGTTATCCACTTATGA
Found at i:17334961 original size:58 final size:58
Alignment explanation
Indices: 17334877--17334987 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
17334867 TTATGGCAAT
* * * *
17334877 CATAATTATTAAATGATGTTGTATTCACTTCAAGG-AATGGATGGATTCATGATCATAC
1 CATAATTATTAAATGATGTCGCATTCACTTC-AGGAAATGGACGAATTCATGATCATAC
*
17334935 CATAATTATTAAATGATGTCGCATTCATTTCAGGAAATGGACGAATTCATGAT
1 CATAATTATTAAATGATGTCGCATTCACTTCAGGAAATGGACGAATTCATGAT
17334988 TTTTTATTAG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 3 0.06
58 44 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (58 bp):
CATAATTATTAAATGATGTCGCATTCACTTCAGGAAATGGACGAATTCATGATCATAC
Found at i:17335983 original size:15 final size:15
Alignment explanation
Indices: 17335950--17335982 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17335940 TTTTTTCTTA
*
17335950 TTTTATTTTTAATAT
1 TTTTAATTTTAATAT
17335965 TTTTAATTTTAAT-T
1 TTTTAATTTTAATAT
17335979 TTTT
1 TTTT
17335983 TCTTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTAATTTTAATAT
Found at i:17337747 original size:19 final size:19
Alignment explanation
Indices: 17337723--17337760 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17337713 CCATTTAACT
17337723 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
17337742 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
17337761 GGTTTGGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:17341131 original size:4 final size:5
Alignment explanation
Indices: 17341091--17341130 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
17341081 TTTCTCGTTA
17341091 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTC -TTTC -TTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
17341131 CCTCCATCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 12 0.35
5 22 0.65
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:17341677 original size:20 final size:20
Alignment explanation
Indices: 17341652--17341697 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
17341642 TTTTGGCCCC
17341652 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
17341672 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
17341692 ATTTGA
1 ATTTGA
17341698 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:17341773 original size:28 final size:27
Alignment explanation
Indices: 17341742--17341794 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
17341732 TTTGGAGTAT
*
17341742 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
17341770 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
17341795 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:17341800 original size:28 final size:28
Alignment explanation
Indices: 17341742--17341800 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
17341732 TTTGGAGTAT
* *
17341742 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
17341770 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
17341798 AGG
1 AGG
17341801 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:17426517 original size:27 final size:28
Alignment explanation
Indices: 17426487--17426539 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
17426477 TGTCTTGCTG
*
17426487 GTGG-AAAATTACAATTTTGCCCCTAGA
1 GTGGCAAAATTACAATTTTACCCCTAGA
*
17426514 GTGGCAAAATTACCATTTTACCCCTA
1 GTGGCAAAATTACAATTTTACCCCTA
17426540 TACTCCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (28 bp):
GTGGCAAAATTACAATTTTACCCCTAGA
Found at i:17426606 original size:19 final size:19
Alignment explanation
Indices: 17426582--17426619 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
17426572 ACTTCTAAAC
17426582 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
*
17426601 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
17426620 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:17434536 original size:47 final size:47
Alignment explanation
Indices: 17434479--17434688 Score: 377
Period size: 47 Copynumber: 4.5 Consensus size: 47
17434469 TGCATACAAG
* *
17434479 TTTACTTAACAAATAAGTAAAATAATTACACCATGCATTTTATAAAT
1 TTTACCTAACAAATAAGTAAAATAATTACACCATGCATTTCATAAAT
*
17434526 TTTACCTAACAAATAAGTAAAATAATTACACCATGCATTTCATAAAA
1 TTTACCTAACAAATAAGTAAAATAATTACACCATGCATTTCATAAAT
*
17434573 TTTACCTAACAAATAAGTAAAATAATTACACCATGCCTTTCATAAAT
1 TTTACCTAACAAATAAGTAAAATAATTACACCATGCATTTCATAAAT
17434620 TTTACCTAACAAATAAGTAAAATAATTACACCATGCATTTCATAAAT
1 TTTACCTAACAAATAAGTAAAATAATTACACCATGCATTTCATAAAT
17434667 TTTACCTAACAAAT-AGTAAAAT
1 TTTACCTAACAAATAAGTAAAAT
17434689 CATACAAAAT
Statistics
Matches: 157, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
46 8 0.05
47 149 0.95
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.32
Consensus pattern (47 bp):
TTTACCTAACAAATAAGTAAAATAATTACACCATGCATTTCATAAAT
Found at i:17442777 original size:21 final size:21
Alignment explanation
Indices: 17442751--17442792 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17442741 TGTTCATGTA
17442751 ATTCATGACAAAGACTGATGC
1 ATTCATGACAAAGACTGATGC
* *
17442772 ATTCATGATAAGGACTGATGC
1 ATTCATGACAAAGACTGATGC
17442793 CTCCATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (21 bp):
ATTCATGACAAAGACTGATGC
Found at i:17447895 original size:28 final size:27
Alignment explanation
Indices: 17447859--17447911 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
17447849 ATATCCTGGT
*
17447859 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
17447886 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
17447912 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:17447979 original size:20 final size:20
Alignment explanation
Indices: 17447956--17448001 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
17447946 CTTCTAAACC
17447956 TCAAATCATACT-TCAATAAG
1 TCAAATCATACTCT-AATAAG
*
17447976 TCAAATTATACTCTAATAAG
1 TCAAATCATACTCTAATAAG
17447996 TCAAAT
1 TCAAAT
17448002 GGGGTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (20 bp):
TCAAATCATACTCTAATAAG
Found at i:17449062 original size:3 final size:3
Alignment explanation
Indices: 17449054--17449103 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
17449044 ACTTTATCTC
* * * * *
17449054 TAG TAG TAG TAG TAG TAG TAG TAA TAA TAA TAA TAA TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
17449102 TA
1 TA
17449104 ATAACTATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:17453351 original size:13 final size:13
Alignment explanation
Indices: 17453333--17453357 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17453323 TTTCAGAAAA
17453333 TTTATAAAATCAT
1 TTTATAAAATCAT
17453346 TTTATAAAATCA
1 TTTATAAAATCA
17453358 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:17461864 original size:5 final size:5
Alignment explanation
Indices: 17461846--17461888 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
17461836 ATTCTATTCT
* *
17461846 ACTTA ACCTG ACTTA ACTTA AC-TA ACTTA ACTTA ACTTA ACTT
1 ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTT
17461889 GGGCCACGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (5 bp):
ACTTA
Found at i:17461943 original size:15 final size:15
Alignment explanation
Indices: 17461923--17461968 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
17461913 TTCTTAAAAC
17461923 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
17461938 AACTTTAAAATCC-AA
1 AACTTTAAAA-CCAAA
* *
17461953 AGCTTTAAAATCAAA
1 AACTTTAAAACCAAA
17461968 A
1 A
17461969 TCTCTTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.89
16 2 0.07
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:17471186 original size:23 final size:23
Alignment explanation
Indices: 17471110--17471243 Score: 92
Period size: 23 Copynumber: 5.8 Consensus size: 23
17471100 ACAGCAGGCC
* *
17471110 ATATGTGACACGACAGGGTTTAGA
1 ATATGTGACACGACATGG-TGAGA
* * * * *
17471134 GTTTGTGAAACGCCATGGTGGGA
1 ATATGTGACACGACATGGTGAGA
17471157 A-AGTGTGACACGACATGGTGAGA
1 ATA-TGTGACACGACATGGTGAGA
* * * *
17471180 GTTTGTGACAC-ACCATGGAGGGA
1 ATATGTGACACGA-CATGGTGAGA
* * *
17471203 ACATGTGACACGGCAGGGTGAGA
1 ATATGTGACACGACATGGTGAGA
*
17471226 ATATGTAACACGACATGG
1 ATATGTGACACGACATGG
17471244 AGAATGGTGA
Statistics
Matches: 79, Mismatches: 27, Indels: 9
0.69 0.23 0.08
Matches are distributed among these distances:
22 1 0.01
23 65 0.82
24 13 0.16
ACGTcount: A:0.31, C:0.15, G:0.34, T:0.21
Consensus pattern (23 bp):
ATATGTGACACGACATGGTGAGA
Found at i:17471196 original size:46 final size:46
Alignment explanation
Indices: 17471112--17471225 Score: 149
Period size: 46 Copynumber: 2.5 Consensus size: 46
17471102 AGCAGGCCAT
* * *
17471112 ATGTGACACGACAGGGTTTAGAGTTTGTGAAACGCCATGGTGGGAA-
1 ATGTGACACGACAGGG-TGAGAGTTTGTGAAACACCATGGAGGGAAC
* *
17471158 AGTGTGACACGACATGGTGAGAGTTTGTGACACACCATGGAGGGAAC
1 A-TGTGACACGACAGGGTGAGAGTTTGTGAAACACCATGGAGGGAAC
*
17471205 ATGTGACACGGCAGGGTGAGA
1 ATGTGACACGACAGGGTGAGA
17471226 ATATGTAACA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
46 44 0.75
47 15 0.25
ACGTcount: A:0.29, C:0.15, G:0.36, T:0.20
Consensus pattern (46 bp):
ATGTGACACGACAGGGTGAGAGTTTGTGAAACACCATGGAGGGAAC
Found at i:17471243 original size:46 final size:45
Alignment explanation
Indices: 17471112--17471245 Score: 137
Period size: 46 Copynumber: 2.9 Consensus size: 45
17471102 AGCAGGCCAT
* * *
17471112 ATGTGACACGACAGGGTTTAGAGTTTGTGAA-ACGCCATGGTGGGAA
1 ATGTGACACGACAGGG-TGAGAGTTTGT-AACACGACATGGAGGGAA
* *
17471158 AGTGTGACACGACATGGTGAGAGTTTGTGACAC-ACCATGGAGGGAA
1 A-TGTGACACGACAGGGTGAGAGTTTGTAACACGA-CATGGAGGGAA
* * *
17471204 CATGTGACACGGCAGGGTGAGAATATGTAACACGACATGGAG
1 -ATGTGACACGACAGGGTGAGAGTTTGTAACACGACATGGAG
17471246 AATGGTGAGA
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
45 1 0.01
46 56 0.77
47 16 0.22
ACGTcount: A:0.31, C:0.15, G:0.34, T:0.20
Consensus pattern (45 bp):
ATGTGACACGACAGGGTGAGAGTTTGTAACACGACATGGAGGGAA
Found at i:17471277 original size:23 final size:23
Alignment explanation
Indices: 17471247--17471356 Score: 93
Period size: 23 Copynumber: 4.9 Consensus size: 23
17471237 GACATGGAGA
*
17471247 ATGGTGAGAATATGTGAGACGCC
1 ATGGTGAGAATATGTGACACGCC
17471270 AAT-GTGAG-A-ATGTGACACGCC
1 -ATGGTGAGAATATGTGACACGCC
* *
17471291 ATGGTGTGAATATGCT-ACATGCC
1 ATGGTGAGAATATG-TGACACGCC
* * * * *
17471314 ATGGTAAGAATATATGAGATGGC
1 ATGGTGAGAATATGTGACACGCC
*
17471337 ATGGTGAGCATATGTGACAC
1 ATGGTGAGAATATGTGACAC
17471357 AGTTGTGACA
Statistics
Matches: 68, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.03
21 15 0.22
22 3 0.04
23 45 0.66
24 3 0.04
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.25
Consensus pattern (23 bp):
ATGGTGAGAATATGTGACACGCC
Found at i:17471499 original size:23 final size:24
Alignment explanation
Indices: 17471473--17471524 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
17471463 TGTGACAATC
*
17471473 CATGGTGGGAA-CGTGTGACACAG
1 CATGGTGGAAATCGTGTGACACAG
* *
17471496 CAT-GTTGAAATCGTGTGAGACAG
1 CATGGTGGAAATCGTGTGACACAG
17471519 CATGGT
1 CATGGT
17471525 CAGAATCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 5 0.21
23 17 0.71
24 2 0.08
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.23
Consensus pattern (24 bp):
CATGGTGGAAATCGTGTGACACAG
Found at i:17472296 original size:31 final size:31
Alignment explanation
Indices: 17472255--17472425 Score: 234
Period size: 31 Copynumber: 5.5 Consensus size: 31
17472245 CTCAACATTG
* * *
17472255 GCGTGTAACAACATTTGACTTGGTATGCTTC
1 GCGTGTAACAACATTTTACTTGGTATGCATA
* * *
17472286 GCATGTAACAACATTTTTCTTGGCATGCATA
1 GCGTGTAACAACATTTTACTTGGTATGCATA
*
17472317 GCGTGTAACAAAATTTTACTTGGTATGCATA
1 GCGTGTAACAACATTTTACTTGGTATGCATA
17472348 GCGTGTAACAACATTTTACTTGGTATGCATA
1 GCGTGTAACAACATTTTACTTGGTATGCATA
** * *
17472379 GCGTGTAACAGTATTTGACTGGGTATGCATA
1 GCGTGTAACAACATTTTACTTGGTATGCATA
*
17472410 GTGTGTAACAACATTT
1 GCGTGTAACAACATTT
17472426 CTTTCTTTCT
Statistics
Matches: 122, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 122 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (31 bp):
GCGTGTAACAACATTTTACTTGGTATGCATA
Found at i:17474155 original size:151 final size:151
Alignment explanation
Indices: 17473893--17474259 Score: 385
Period size: 151 Copynumber: 2.4 Consensus size: 151
17473883 TTATGGATTA
* * * * *
17473893 TGTTCAATAATTCTATATGTGATTATCGAATAACACAATAATTTCTATTATTGTAGTTGACCGAT
1 TGTTCAACAATTCCATATATGATTATCGAATAACACAATAATTTCTATTATTGCAGTTGACCAAT
* * ** * * *
17473958 AAGATGACAGCTTTTCAACCACTAACAAGTCCTATTCAGACACACAGTGCTAA-CAATCCACTAG
66 AAGACGACAACTCCTCAACCACCAACAAGTCCTACTCAGACACACAGAGCTAATCAATCCAC-AG
** *
17474022 TAAAAATGGTTCTAATTGTTTG
130 TAAAAACAGTTCTAACTGTTTG
* * * * *
17474044 TGTTCAACAATTCCATATATGATTATCAAATAACACAATAATTTTTGTTATTGCAGTTGGCTAAT
1 TGTTCAACAATTCCATATATGATTATCGAATAACACAATAATTTCTATTATTGCAGTTGACCAAT
* * * ** * * ***
17474109 GAGACGACAACTCCTCAACCACCAACAGGTCCTGCTCAGATGCACAGAGCTAATGAGTTGTCAGT
66 AAGACGACAACTCCTCAACCACCAACAAGTCCTACTCAGACACACAGAGCTAATCAATCCACAGT
* *
17474174 AAGAACAGTTTTAACTGTTTG
131 AAAAACAGTTCTAACTGTTTG
* * * **
17474195 TGTTCAACAATTTCATATATGATTATCGAATAACATAGTAATTTCTATTATTATAGTTGACCAAT
1 TGTTCAACAATTCCATATATGATTATCGAATAACACAATAATTTCTATTATTGCAGTTGACCAAT
17474260 GCGACGATAG
Statistics
Matches: 173, Mismatches: 42, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
151 170 0.98
152 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (151 bp):
TGTTCAACAATTCCATATATGATTATCGAATAACACAATAATTTCTATTATTGCAGTTGACCAAT
AAGACGACAACTCCTCAACCACCAACAAGTCCTACTCAGACACACAGAGCTAATCAATCCACAGT
AAAAACAGTTCTAACTGTTTG
Found at i:17474294 original size:151 final size:154
Alignment explanation
Indices: 17474030--17474414 Score: 364
Period size: 151 Copynumber: 2.5 Consensus size: 154
17474020 AGTAAAAATG
* * * * * * *
17474030 GTTCTAATTGTTTGTGTTCAACAATTCCATATATGATTATCAAATAACACAATAATTTTTGTTAT
1 GTTCTAACTGTTTGTGTTCAACAATTTCATATATGATTATCGAATAACATAGTAATTTCTATTAT
* * * * ** * *
17474095 TGCAGTTGGCTAATGAGACGACAACTCCTCAACCACCAACAGGTCCTGCTCAGATGCACAGAGCT
66 TACAGTTGACCAATGAGACGACAACTCCTCAACCAACAACAGAACCTGCTCAAACGCACAGAGCT
* **** *
17474160 AATGAGTTGTCAGTAA-G-A-ACA
131 AACGAGCCACCAGTAAGGAATAAA
*
17474181 GTTTTAACTGTTTGTGTTCAACAATTTCATATATGATTATCGAATAACATAGTAATTTCTATTAT
1 GTTCTAACTGTTTGTGTTCAACAATTTCATATATGATTATCGAATAACATAGTAATTTCTATTAT
* * * * * * ** *
17474246 TATAGTTGACCAATGCGACGATAGCTCTTTAACCAATGACAGAACCTGCTCAAACGCACAGTGCT
66 TACAGTTGACCAATGAGACGACAACTCCTCAACCAACAACAGAACCTGCTCAAACGCACAGAGCT
*
17474311 AACGAGCCACCGGTAAGGATATTAAA
131 AACGAGCCACCAGTAAGGA-A-TAAA
* * * * * *
17474337 GTTCTAACAGTTTATGTTCAACAATTTCAT-TATGATTATTGAATAACATAGTAATATATGTTAT
1 GTTCTAACTGTTTGTGTTCAACAATTTCATATATGATTATCGAATAACATAGTAATTTCTATTAT
* *
17474401 TGCAGTTAACCAAT
66 TACAGTTGACCAAT
17474415 TTGACGAAAG
Statistics
Matches: 187, Mismatches: 42, Indels: 6
0.80 0.18 0.03
Matches are distributed among these distances:
151 115 0.61
152 1 0.01
154 1 0.01
155 41 0.22
156 29 0.16
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (154 bp):
GTTCTAACTGTTTGTGTTCAACAATTTCATATATGATTATCGAATAACATAGTAATTTCTATTAT
TACAGTTGACCAATGAGACGACAACTCCTCAACCAACAACAGAACCTGCTCAAACGCACAGAGCT
AACGAGCCACCAGTAAGGAATAAA
Found at i:17475045 original size:81 final size:81
Alignment explanation
Indices: 17474904--17475088 Score: 219
Period size: 81 Copynumber: 2.3 Consensus size: 81
17474894 GATGCTGAAG
* * * * * * *
17474904 GAGACCATGTTCCTTAGGTCGATGTGGTTGTTGATGAATATGCGAGAGGGGAAGGAGACCTTCAA
1 GAGACCATGTTCCTCAGGTTGATGTGGTTATCGATGAATATGCCAAAGGGAAAGGAGACCTTCAA
*
17474969 TTAGTTGAGGTTGAAAA
66 TTAGTTGAGGCT-AAAA
* * * * *
17474986 -AGACCATATTCCTCAGGTTGATGTGGTTATCGATGCATTTGCCAAAGGGAAAGGGGACCTTCAC
1 GAGACCATGTTCCTCAGGTTGATGTGGTTATCGATGAATATGCCAAAGGGAAAGGAGACCTTCAA
17475050 TTAGTTGAGGCTAAAA
66 TTAGTTGAGGCTAAAA
* *
17475066 GTGACCATGTTCCTCAGGCTGAT
1 GAGACCATGTTCCTCAGGTTGAT
17475089 TCGATAGTCA
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
80 4 0.05
81 82 0.95
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (81 bp):
GAGACCATGTTCCTCAGGTTGATGTGGTTATCGATGAATATGCCAAAGGGAAAGGAGACCTTCAA
TTAGTTGAGGCTAAAA
Found at i:17476847 original size:76 final size:76
Alignment explanation
Indices: 17476740--17477491 Score: 715
Period size: 76 Copynumber: 10.0 Consensus size: 76
17476730 CTAACAAGCA
* * * * ** *
17476740 TGGCATGTCACCTCATAATACTGCAACGACTCAATGTGTCACCGTAAGATGTCAACAACATCTAA
1 TGGCGTGTCACCCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
* *
17476805 CAATTAGAACA
66 CAATTGGAACG
* * * * * * * *
17476816 TGGTGTGTCACCCTATAATACTACAACGACTCAGCATGTTACCACTAGATGTCAACGACATCTAA
1 TGGCGTGTCACCCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
17476881 CAATTGGAACG
66 CAATTGGAACG
** ** * *
17476892 TGTTGTGTCACCCCATAATACCACAACCACTCAACGTGTCACCACAAGATGTCAAGGACATTTAA
1 TGGCGTGTCACCCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
*
17476957 CAATTGGAATG
66 CAATTGGAACG
* * * *
17476968 TGACGTGTCACCCCATAATACTGTAACCACTCAACGTGCCACCACAAGATGTCAACAACATCTAA
1 TGGCGTGTCACCCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
17477033 CAATT-GAAGCG
66 CAATTGGAA-CG
* * * **
17477044 TGGCATGTCACCCCATAATACTGCAACCACTTAACGTGTCACCATAAGATGTCAACGGTATCTAA
1 TGGCGTGTCACCCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
* *
17477109 CAATTGGAGCA
66 CAATTGGAACG
* * * ** * ** *
17477120 TGGCATTTCACCCCATAATACTACAATGACTCAACGTGCCATTACAAGATGTCAACGACATTTAA
1 TGGCGTGTCACCCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
* *
17477185 CAATTAGAGCG
66 CAATTGGAACG
* * * *
17477196 TGGCGTGTCACCCCATAATACTGCAACAACTCAACGTGCCACCACAAGATTTCAATGACATCTAA
1 TGGCGTGTCACCCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
* *
17477261 CAATTGGAGCA
66 CAATTGGAACG
* * * * * * *
17477272 TGACATTTCACCCCATAATACTGCAACCGCTCAGCGTGTCACCACAAGATGTTAATGACATCTAA
1 TGGCGTGTCACCCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
** *
17477337 CAAACGGAATG
66 CAATTGGAACG
* * * * * * *
17477348 CGACATGTCACCCCATAATACTGCAACCATTCAACATGTCACAACAAGATGTCAACGACATTTAA
1 TGGCGTGTCACCCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
*
17477413 CAA---G--CA
66 CAATTGGAACG
* * * * * ** * * * * *
17477419 TGGCGTGTCAACCTAAAATACTGCAACGACACGGCATCTCACCACAAGATGTAAACGACATGTTA
1 TGGCGTGTCACCCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
17477484 CAATTGGA
66 CAATTGGA
17477492 GCATGTAATA
Statistics
Matches: 555, Mismatches: 115, Indels: 13
0.81 0.17 0.02
Matches are distributed among these distances:
71 52 0.09
73 1 0.00
74 1 0.00
75 3 0.01
76 496 0.89
77 2 0.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (76 bp):
TGGCGTGTCACCCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCAACGACATCTAA
CAATTGGAACG
Found at i:17477154 original size:228 final size:227
Alignment explanation
Indices: 17476745--17477415 Score: 799
Period size: 228 Copynumber: 2.9 Consensus size: 227
17476735 AAGCATGGCA
* * * * **
17476745 TGTCACCTCATAATACTGCAACGACTCAATGTGTCACCGTAAGATGTCAACAACATCTAACAATT
1 TGTCACCCCATAATACTGCAACAACTCAACGTGCCACCACAAGATGTCAACAACATCTAACAATT
** * * * * *
17476810 AGAA-CATGGTGTGTCACCCTATAATACTACAACGACTCAGCATGTTACCACT-AGATGTCAACG
66 -GAAGCATGGCATGTCACCCCATAATACTGCAACCACTCAGCGTGTCACCA-TAAGATGTCAACG
* *** * *
17476873 ACATCTAACAATTGGAACGTGTTGTGTCACCCCATAATACCACAACCACTCAACGTGTCACCACA
129 ACATCTAACAATTGG-ACATGGCATGTCACCCCATAATACTACAACCACTCAACGTGTCACAACA
* * *
17476938 AGATGTCAAGGACATTTAACAATTGGAATGTGACG
193 AGATGTCAACGACATTTAACAATTAGAACGTGACG
* *
17476973 TGTCACCCCATAATACTGTAACCACTCAACGTGCCACCACAAGATGTCAACAACATCTAACAATT
1 TGTCACCCCATAATACTGCAACAACTCAACGTGCCACCACAAGATGTCAACAACATCTAACAATT
* * * **
17477038 GAAGCGTGGCATGTCACCCCATAATACTGCAACCACTTAACGTGTCACCATAAGATGTCAACGGT
66 GAAGCATGGCATGTCACCCCATAATACTGCAACCACTCAGCGTGTCACCATAAGATGTCAACGAC
* ** * **
17477103 ATCTAACAATTGGAGCATGGCATTTCACCCCATAATACTACAATGACTCAACGTGCCATTACAAG
131 ATCTAACAATTGGA-CATGGCATGTCACCCCATAATACTACAACCACTCAACGTGTCACAACAAG
* *
17477168 ATGTCAACGACATTTAACAATTAGAGCGTGGCG
195 ATGTCAACGACATTTAACAATTAGAACGTGACG
* **
17477201 TGTCACCCCATAATACTGCAACAACTCAACGTGCCACCACAAGATTTCAATGACATCTAACAATT
1 TGTCACCCCATAATACTGCAACAACTCAACGTGCCACCACAAGATGTCAACAACATCTAACAATT
* * * * * * *
17477266 GGAGCATGACATTTCACCCCATAATACTGCAACCGCTCAGCGTGTCACCACAAGATGTTAATGAC
66 GAAGCATGGCATGTCACCCCATAATACTGCAACCACTCAGCGTGTCACCATAAGATGTCAACGAC
** * * *
17477331 ATCTAACAAACGGA-ATGCGACATGTCACCCCATAATACTGCAACCATTCAACATGTCACAACAA
131 ATCTAACAATTGGACATG-G-CATGTCACCCCATAATACTACAACCACTCAACGTGTCACAACAA
17477395 GATGTCAACGACATTTAACAA
194 GATGTCAACGACATTTAACAA
17477416 GCATGGCGTG
Statistics
Matches: 375, Mismatches: 63, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
226 3 0.01
227 6 0.02
228 366 0.98
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (227 bp):
TGTCACCCCATAATACTGCAACAACTCAACGTGCCACCACAAGATGTCAACAACATCTAACAATT
GAAGCATGGCATGTCACCCCATAATACTGCAACCACTCAGCGTGTCACCATAAGATGTCAACGAC
ATCTAACAATTGGACATGGCATGTCACCCCATAATACTACAACCACTCAACGTGTCACAACAAGA
TGTCAACGACATTTAACAATTAGAACGTGACG
Found at i:17478496 original size:30 final size:30
Alignment explanation
Indices: 17478462--17478532 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
17478452 TTTAACAGTT
17478462 TTCTAGCCGTTGGAGACAGTTGAGAGTCAG
1 TTCTAGCCGTTGGAGACAGTTGAGAGTCAG
17478492 TTCTAGCCGTTGGAGACAGTTGAGAGTCAG
1 TTCTAGCCGTTGGAGACAGTTGAGAGTCAG
17478522 TTCTAGCCGTT
1 TTCTAGCCGTT
17478533 ACTTTGTCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (30 bp):
TTCTAGCCGTTGGAGACAGTTGAGAGTCAG
Found at i:17498758 original size:23 final size:23
Alignment explanation
Indices: 17498732--17498817 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
17498722 TCAATCATGT
17498732 TGTTACACGCCATGTTCAAAAAA
1 TGTTACACGCCATGTTCAAAAAA
* * *
17498755 TGTTACATGCCATATTCAAAATA
1 TGTTACACGCCATGTTCAAAAAA
*
17498778 TGTTACATGCCATGTTCAATAAAAA
1 TGTTACACGCCATGTTC-A-AAAAA
*
17498803 TGTTACACACCATGT
1 TGTTACACGCCATGT
17498818 GCTAATACAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 36 0.67
24 1 0.02
25 17 0.31
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (23 bp):
TGTTACACGCCATGTTCAAAAAA
Found at i:17501238 original size:39 final size:38
Alignment explanation
Indices: 17501188--17501286 Score: 126
Period size: 38 Copynumber: 2.6 Consensus size: 38
17501178 AGGTAAAAAT
* * ** *
17501188 TTTTAAGTTAAATGTTGGTATTTTAAATTTTTTTTAATA
1 TTTTAACTTAAATATTAATATTTTAAA-GTTTTTTAATA
* *
17501227 TTTTAATTTAAATATTAATATTTTTAAGTTTTTTAATA
1 TTTTAACTTAAATATTAATATTTTAAAGTTTTTTAATA
17501265 TTTTAACTTAAATATTAATATT
1 TTTTAACTTAAATATTAATATT
17501287 CTTCAAACAT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 31 0.58
39 22 0.42
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (38 bp):
TTTTAACTTAAATATTAATATTTTAAAGTTTTTTAATA
Found at i:17501246 original size:20 final size:20
Alignment explanation
Indices: 17501221--17501286 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
17501211 TAAATTTTTT
17501221 TTAATATTTTAATTTAAATA
1 TTAATATTTTAATTTAAATA
17501241 TTAATATTTTTAAGTTT---T-
1 TTAATA-TTTTAA-TTTAAATA
*
17501259 TTAATATTTTAACTTAAATA
1 TTAATATTTTAATTTAAATA
17501279 TTAATATT
1 TTAATATT
17501287 CTTCAAACAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
16 2 0.05
17 6 0.15
18 6 0.15
19 2 0.05
20 14 0.36
21 6 0.15
22 3 0.08
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TTAATATTTTAATTTAAATA
Found at i:17509431 original size:2 final size:2
Alignment explanation
Indices: 17509424--17509448 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17509414 NNNNNNNNNN
17509424 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17509449 GTTTTACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17513814 original size:27 final size:27
Alignment explanation
Indices: 17513763--17513814 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
17513753 ATGTCCTGGT
*
17513763 GGTGGAAAATTACAATTTTGCCCCTAG
1 GGTGGAAAATTACAATTTTGACCCTAG
17513790 GGTGGCAAAATTATC-ATTTT-ACCCT
1 GGTGG-AAAATTA-CAATTTTGACCCT
17513815 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 9 0.41
28 12 0.55
29 1 0.05
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTAG
Found at i:17513885 original size:20 final size:20
Alignment explanation
Indices: 17513860--17513905 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
17513850 CTTCTAAACC
*
17513860 TCAAATCCTACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
17513880 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
17513900 TCAAAT
1 TCAAAT
17513906 GGGGCCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:17515767 original size:23 final size:23
Alignment explanation
Indices: 17515741--17515793 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
17515731 TATATATATT
17515741 ATTGTGAAATGGAAAAGCCTCTA
1 ATTGTGAAATGGAAAAGCCTCTA
*
17515764 ATTGTGAAATGGAAAAGCCTTTA
1 ATTGTGAAATGGAAAAGCCTCTA
17515787 ATTGTGA
1 ATTGTGA
17515794 CCACCTCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (23 bp):
ATTGTGAAATGGAAAAGCCTCTA
Found at i:17532033 original size:25 final size:24
Alignment explanation
Indices: 17531959--17532044 Score: 113
Period size: 23 Copynumber: 3.6 Consensus size: 24
17531949 TCAGTCATGT
17531959 TGTTACACGCCATGTTCA-AAAAA
1 TGTTACACGCCATGTTCATAAAAA
* * *
17531982 TGTTACACGTCATATTC-TAAATA
1 TGTTACACGCCATGTTCATAAAAA
17532005 TGTTACACGCCATGTTCAATAAAAA
1 TGTTACACGCCATGTTC-ATAAAAA
*
17532030 TGTTACAAGCCATGT
1 TGTTACACGCCATGT
17532045 GCTAACACAT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 34 0.64
25 19 0.36
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (24 bp):
TGTTACACGCCATGTTCATAAAAA
Found at i:17532379 original size:63 final size:63
Alignment explanation
Indices: 17532276--17532399 Score: 140
Period size: 63 Copynumber: 2.0 Consensus size: 63
17532266 ACCATAACAC
* * *
17532276 AATGACGATGGTGCTCAACAGAAAGTTGACAAAACTGATACAATTCAGAGAGCTAAGAGAGCT
1 AATGACAATGGTGCTCAACAGAAAGTTGACAAAACAGATACAATTCAAAGAGCTAAGAGAGCT
* * * * * * * * *
17532339 AATGACAATGGTGTTCAATAGAGAGTTGATAGAGCAGATACAGTTCAAAGAGTTGAGAGAG
1 AATGACAATGGTGCTCAACAGAAAGTTGACAAAACAGATACAATTCAAAGAGCTAAGAGAG
17532400 TTGAGCAAGT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (63 bp):
AATGACAATGGTGCTCAACAGAAAGTTGACAAAACAGATACAATTCAAAGAGCTAAGAGAGCT
Found at i:17535526 original size:20 final size:20
Alignment explanation
Indices: 17535501--17535546 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
17535491 TTTTGACCCC
17535501 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
17535521 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
17535541 ATTTGA
1 ATTTGA
17535547 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:17535622 original size:28 final size:27
Alignment explanation
Indices: 17535591--17535643 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
17535581 TTTGGAGTAT
*
17535591 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
17535619 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
17535644 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:17535649 original size:28 final size:28
Alignment explanation
Indices: 17535591--17535649 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
17535581 TTTGGAGTAT
* *
17535591 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
17535619 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
17535647 AGG
1 AGG
17535650 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:17540017 original size:19 final size:19
Alignment explanation
Indices: 17539993--17540030 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17539983 CCATTTGACT
17539993 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
17540012 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
17540031 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:17540130 original size:28 final size:28
Alignment explanation
Indices: 17540073--17540131 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
17540063 ATCGGAGTAT
*
17540073 AGGGGTAAAATGGTAATTTTGCCACTCC
1 AGGGGTAAAATGGTAATTTTGCCACACC
* *
17540101 AGGGGTAAATTTGTAATTTT-CCACCACC
1 AGGGGTAAAATGGTAATTTTGCCA-CACC
17540129 AGG
1 AGG
17540132 ACAATTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (28 bp):
AGGGGTAAAATGGTAATTTTGCCACACC
Found at i:17542496 original size:9 final size:10
Alignment explanation
Indices: 17542475--17542503 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
17542465 CTAAGGTAGT
17542475 TTTTATGAAA
1 TTTTATGAAA
17542485 TTTTAT-AAA
1 TTTTATGAAA
17542494 TTTTATGAAA
1 TTTTATGAAA
17542504 AATGGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TTTTATGAAA
Found at i:17558384 original size:61 final size:60
Alignment explanation
Indices: 17558257--17558393 Score: 168
Period size: 61 Copynumber: 2.3 Consensus size: 60
17558247 ACAGAAAGTT
* * * * * * *
17558257 TTTCGCTACAGCGAAATTTCTACCCAGAAACAGAATGTTTCTCGCTGCAGCGAGATTCAA
1 TTTCGCTACAGCGAAATTGCAACCCAGAAACAAAAAGTTTCTCACTGCAGCAAGATGCAA
* *
17558317 TCTCGCTGCAGCGAAATTGCAACCCAGAAAACAAAAAGTTTCTCACTGCAGCAAGAATGC-A
1 TTTCGCTACAGCGAAATTGCAACCCAG-AAACAAAAAGTTTCTCACTGCAGCAAG-ATGCAA
17558378 TTTCGCTACAGCGAAA
1 TTTCGCTACAGCGAAA
17558394 AGCTACAGTG
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
60 23 0.36
61 38 0.59
62 3 0.05
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (60 bp):
TTTCGCTACAGCGAAATTGCAACCCAGAAACAAAAAGTTTCTCACTGCAGCAAGATGCAA
Found at i:17558687 original size:2 final size:2
Alignment explanation
Indices: 17558682--17558711 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17558672 CACACACACG
*
17558682 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17558712 CCCATCATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:17558811 original size:43 final size:43
Alignment explanation
Indices: 17558763--17558870 Score: 146
Period size: 43 Copynumber: 2.5 Consensus size: 43
17558753 TCACTAGCTC
** *
17558763 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCATCGAG-TT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCATCG-GCTT
* *
17558806 ATGCGCACTTCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCATCGGCTT
*
17558849 ATGTGCACTCCCTACTCGCACA
1 ATGCGCACTCCCTACTCGCACA
17558871 GAGCCGAGTC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.02
43 56 0.98
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCATCGGCTT
Found at i:17559701 original size:19 final size:20
Alignment explanation
Indices: 17559667--17559704 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
17559657 GAAGAAGACT
*
17559667 AGCTGCTGGAAAATTCAAGA
1 AGCTGCTAGAAAATTCAAGA
17559687 AGCTGCTAG-AAATTCAAG
1 AGCTGCTAGAAAATTCAAG
17559705 GTATTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (20 bp):
AGCTGCTAGAAAATTCAAGA
Found at i:17574240 original size:19 final size:19
Alignment explanation
Indices: 17574216--17574253 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
17574206 CTGTCAAACC
*
17574216 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
17574235 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
17574254 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:17581037 original size:28 final size:29
Alignment explanation
Indices: 17580996--17581055 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
17580986 GTCTATGGGC
*
17580996 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
17581024 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
17581054 AA
1 AA
17581056 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:17597177 original size:23 final size:23
Alignment explanation
Indices: 17597149--17597226 Score: 111
Period size: 23 Copynumber: 3.3 Consensus size: 23
17597139 TCAATCATGT
17597149 TGTTACACGCCATGTTCAAAAAA
1 TGTTACACGCCATGTTCAAAAAA
* * *
17597172 TGTTACACGCCATATTGAAAATA
1 TGTTACACGCCATGTTCAAAAAA
17597195 TGTTACACGCCATGTTCAATAAAAA
1 TGTTACACGCCATGTTC-A-AAAAA
17597220 TGTTACA
1 TGTTACA
17597227 ATCCATGTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 35 0.74
24 1 0.02
25 11 0.23
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (23 bp):
TGTTACACGCCATGTTCAAAAAA
Found at i:17602621 original size:49 final size:49
Alignment explanation
Indices: 17602558--17602666 Score: 173
Period size: 49 Copynumber: 2.2 Consensus size: 49
17602548 ACTTCATTCA
* *
17602558 TCATCATAGTCGGGTCATCATCATCATCGGCTTATGCGCACTTCCTACTC
1 TCAT-ATAGCCGGGTCATCATCATCATCGGCTTATGCGCACTCCCTACTC
17602608 TCATATAGCCGGGTCATCATCATCATCGGCTTATGCGCACTCCCTACTC
1 TCATATAGCCGGGTCATCATCATCATCGGCTTATGCGCACTCCCTACTC
* *
17602657 GCACATAGCC
1 TCATATAGCC
17602667 AAGTCAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
49 51 0.93
50 4 0.07
ACGTcount: A:0.21, C:0.34, G:0.17, T:0.28
Consensus pattern (49 bp):
TCATATAGCCGGGTCATCATCATCATCGGCTTATGCGCACTCCCTACTC
Found at i:17602679 original size:49 final size:49
Alignment explanation
Indices: 17602571--17602681 Score: 161
Period size: 49 Copynumber: 2.3 Consensus size: 49
17602561 TCATAGTCGG
* * * **
17602571 GTCATCATCATCATCGGCTTATGCGCACTTCCTACTCTCATATAGCCGG
1 GTCATCATCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCAA
17602620 GTCATCATCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCAA
1 GTCATCATCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCAA
17602669 GTCAAT-ATCATCA
1 GTC-ATCATCATCA
17602682 CACAACATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 54 0.96
50 2 0.04
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.28
Consensus pattern (49 bp):
GTCATCATCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCAA
Found at i:17609032 original size:25 final size:23
Alignment explanation
Indices: 17608950--17609035 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
17608940 TCAGTCATGT
* *
17608950 TGTTACACACCACGTTCAAAAAA
1 TGTTACACGCCATGTTCAAAAAA
* *
17608973 TGTTACACGCCATATTCAAAATA
1 TGTTACACGCCATGTTCAAAAAA
17608996 TGTTACACGCCATGTTCAATAAAAA
1 TGTTACACGCCATGTTC-A-AAAAA
*
17609021 TGTTACAAGCCATGT
1 TGTTACACGCCATGT
17609036 GCCAACACAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 35 0.65
24 1 0.02
25 18 0.33
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (23 bp):
TGTTACACGCCATGTTCAAAAAA
Found at i:17610895 original size:19 final size:20
Alignment explanation
Indices: 17610868--17610913 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
17610858 AGGAGACAAG
*
17610868 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
17610887 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
17610906 ATAATATT
1 ATAATATT
17610914 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:17611416 original size:28 final size:27
Alignment explanation
Indices: 17611385--17611437 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
17611375 TTTGGAGTAA
* *
17611385 AAGGGTAAAATGGTAATTTTACCACCCT
1 AAGGGCAAAATGGCAATTTT-CCACCCT
*
17611413 AAGGGCAAAATTGCAATTTTCCACC
1 AAGGGCAAAATGGCAATTTTCCACC
17611438 ACCAGGACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (27 bp):
AAGGGCAAAATGGCAATTTTCCACCCT
Found at i:17612594 original size:13 final size:13
Alignment explanation
Indices: 17612576--17612600 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17612566 AGAGAAATTG
17612576 TGATTTTATAAAA
1 TGATTTTATAAAA
17612589 TGATTTTATAAA
1 TGATTTTATAAA
17612601 TTTTCTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:17619206 original size:13 final size:13
Alignment explanation
Indices: 17619188--17619212 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17619178 AGAGAAATTG
17619188 TGATTTTATAAAA
1 TGATTTTATAAAA
17619201 TGATTTTATAAA
1 TGATTTTATAAA
17619213 TTTTCTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:17621399 original size:39 final size:39
Alignment explanation
Indices: 17621344--17621443 Score: 157
Period size: 38 Copynumber: 2.6 Consensus size: 39
17621334 GTTAAAAAAA
*
17621344 ATTTTAAGTTAAATATTAGTATTTTTTAACTTTTTTAAT
1 ATTTTAAGTTAAATATTAATATTTTTTAACTTTTTTAAT
* *
17621383 GTTTTAAGTTAAATATTAATA-TTTTTAAGTTTTTTAAT
1 ATTTTAAGTTAAATATTAATATTTTTTAACTTTTTTAAT
*
17621421 ATTTTAACTTAAATATTAATATT
1 ATTTTAAGTTAAATATTAATATT
17621444 CTTCAAACAT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 35 0.64
39 20 0.36
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (39 bp):
ATTTTAAGTTAAATATTAATATTTTTTAACTTTTTTAAT
Found at i:17625863 original size:3 final size:3
Alignment explanation
Indices: 17625855--17625879 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17625845 CACTAAATTG
17625855 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
17625880 ATATAATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:17627899 original size:58 final size:58
Alignment explanation
Indices: 17627809--17627924 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 58
17627799 TCGAGAAGAT
*
17627809 TTAGCAGCAAGGTTGCAAAGCTTGGCATGTGAGTTTACCAAGTTCAATAGTAGGGGGA
1 TTAGCAGCAAGGTTGCAAAGCTTGGCACGTGAGTTTACCAAGTTCAATAGTAGGGGGA
* * *
17627867 TTAGCAGCAAGGTTGCATAGCTTGGCACGTGAGTTTACCAAGTTTAGTAGTAGGGGGA
1 TTAGCAGCAAGGTTGCAAAGCTTGGCACGTGAGTTTACCAAGTTCAATAGTAGGGGGA
17627925 GTACAGTTAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.27
Consensus pattern (58 bp):
TTAGCAGCAAGGTTGCAAAGCTTGGCACGTGAGTTTACCAAGTTCAATAGTAGGGGGA
Found at i:17637646 original size:20 final size:20
Alignment explanation
Indices: 17637621--17637666 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
17637611 CTTCTAAACC
17637621 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
* *
17637641 TCAAATTATACTCCAATGAG
1 TCAAATCATACTCCAATAAG
17637661 TCAAAT
1 TCAAAT
17637667 GGGGCCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:17651957 original size:28 final size:28
Alignment explanation
Indices: 17651916--17651986 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
17651906 CATTAAAGTA
*
17651916 TAACAA-AATGTTTTTAAATATAGCATG
1 TAACAATAATATTTTTAAATATAGCATG
* * *
17651943 TAACAATAATATTTTTCAATATGGCGTG
1 TAACAATAATATTTTTAAATATAGCATG
17651971 TAACAATAATATTTTT
1 TAACAATAATATTTTT
17651987 TCAACATAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 6 0.15
28 33 0.85
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (28 bp):
TAACAATAATATTTTTAAATATAGCATG
Found at i:17652003 original size:23 final size:24
Alignment explanation
Indices: 17651977--17652026 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
17651967 CGTGTAACAA
17651977 TAATAT-TTTTTCAACATAACGTG
1 TAATATATTTTTCAACATAACGTG
* **
17652000 TAATATATTTTTGAACATGGCGTG
1 TAATATATTTTTCAACATAACGTG
17652024 TAA
1 TAA
17652027 CAATAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (24 bp):
TAATATATTTTTCAACATAACGTG
Found at i:17652076 original size:26 final size:26
Alignment explanation
Indices: 17652035--17652118 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
17652025 AACAATAATT
17652035 TTTTTTTTGAAT-ATGATATGTAACAA
1 TTTTTTTT-AATCATGATATGTAACAA
** *
17652061 TTTTTTTTAATCATGACGTATAAC-A
1 TTTTTTTTAATCATGATATGTAACAA
**
17652086 -TGCTTTT-ATACATGATATGTAACATA
1 TTTTTTTTAAT-CATGATATGTAACA-A
17652112 TTTTTTT
1 TTTTTTT
17652119 ATATGACGTG
Statistics
Matches: 43, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
23 2 0.05
24 15 0.35
25 4 0.09
26 18 0.42
27 4 0.09
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (26 bp):
TTTTTTTTAATCATGATATGTAACAA
Found at i:17652124 original size:24 final size:25
Alignment explanation
Indices: 17652036--17652133 Score: 67
Period size: 24 Copynumber: 3.9 Consensus size: 25
17652026 ACAATAATTT
*
17652036 TTTTTTTGAATATGATATGTAACA-A
1 TTTTTTT-AATATGACATGTAACATA
* * *
17652061 TTTTTTTTAATCATGACGTATAACATG
1 -TTTTTTTAAT-ATGACATGTAACATA
* * * *
17652088 CTTTTAT-ACATGATATGTAACATA
1 TTTTTTTAATATGACATGTAACATA
*
17652112 TTTTTTT-ATATGACGTGTAACA
1 TTTTTTTAATATGACATGTAACA
17652134 ACTTAATTAT
Statistics
Matches: 54, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
24 28 0.52
25 4 0.07
26 22 0.41
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (25 bp):
TTTTTTTAATATGACATGTAACATA
Found at i:17652235 original size:15 final size:15
Alignment explanation
Indices: 17652212--17652267 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
17652202 AAATAATTAA
* *
17652212 ATTTATAAAAAAATT
1 ATTTTTAAAAAATTT
17652227 ATTTTTAAAAACATTT
1 ATTTTTAAAAA-ATTT
*
17652243 AATCTTT--AAAATTT
1 -ATTTTTAAAAAATTT
17652257 ATTTTTAAAAA
1 ATTTTTAAAAA
17652268 TGTCCTGCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 5 0.15
14 4 0.12
15 16 0.48
16 3 0.09
17 5 0.15
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTTTTAAAAAATTT
Found at i:17655453 original size:68 final size:69
Alignment explanation
Indices: 17655380--17655516 Score: 242
Period size: 69 Copynumber: 2.0 Consensus size: 69
17655370 TTTGACTTCC
17655380 AAAATTTGAGATTATTTTTC-TGTTTTTCTTATAGAGTAAACCCAAATTTTAAAATTAG-TTTTC
1 AAAATTTGAGATTATTTTTCTTGTTTTTCTTATAGAGTAAACCCAAATTTTAAAATT-GTTTTTC
17655443 TAATT
65 TAATT
*
17655448 AAAATTTGAGATTATTTTTCTTTTTTTTCTTATAGAGTAAACCCAAATTTTAAAATTGTTTTTCT
1 AAAATTTGAGATTATTTTTCTTGTTTTTCTTATAGAGTAAACCCAAATTTTAAAATTGTTTTTCT
17655513 AATT
66 AATT
17655517 TTTCTTTTTT
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
68 21 0.32
69 45 0.68
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.50
Consensus pattern (69 bp):
AAAATTTGAGATTATTTTTCTTGTTTTTCTTATAGAGTAAACCCAAATTTTAAAATTGTTTTTCT
AATT
Found at i:17655576 original size:79 final size:75
Alignment explanation
Indices: 17655481--17655631 Score: 212
Period size: 79 Copynumber: 2.0 Consensus size: 75
17655471 TTTTTCTTAT
* *
17655481 AGAGTAAACCCAAATTTTAAAATTGTTTTTCTAATTTTTCTTTTTTCTTATAGAGTAAAAGATGC
1 AGAGTAAACCCAAATTTTAAAATTATTTTTCTAA-TTTTC---TTTCTTATAAAGTAAAAGATGC
*
17655546 ATTGCTTAACTAAA
62 ATTACTTAACTAAA
* * *
17655560 AGAGTAAACCCAAATTTTGAAATTATTTTTCTTATTTTCTTTCTTATAAAGTAGAAGATGCATTA
1 AGAGTAAACCCAAATTTTAAAATTATTTTTCTAATTTTCTTTCTTATAAAGTAAAAGATGCATTA
17655625 CTTAACT
66 CTTAACT
17655632 CTATCTAAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
75 30 0.45
78 5 0.08
79 31 0.47
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (75 bp):
AGAGTAAACCCAAATTTTAAAATTATTTTTCTAATTTTCTTTCTTATAAAGTAAAAGATGCATTA
CTTAACTAAA
Found at i:17674893 original size:28 final size:30
Alignment explanation
Indices: 17674833--17674895 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 30
17674823 TGCTCAAGAC
* *
17674833 TATTTATTGTTGTTTTTATCTATGTTTTTAAT
1 TATTTATTGTTGTTTTTATCTA--TTATAAAT
17674865 TATTTATTGTTGTTTTTATC-A-TATAAAT
1 TATTTATTGTTGTTTTTATCTATTATAAAT
17674893 TAT
1 TAT
17674896 ATGAGTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 8 0.28
31 1 0.03
32 20 0.69
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.65
Consensus pattern (30 bp):
TATTTATTGTTGTTTTTATCTATTATAAAT
Found at i:17675403 original size:69 final size:68
Alignment explanation
Indices: 17675317--17675456 Score: 253
Period size: 69 Copynumber: 2.0 Consensus size: 68
17675307 ATATAAATGG
* *
17675317 TATATTATCTATATTGACCTTATATATAATATACATAATTTTATTTATGTATTAATGTTAACATT
1 TATATTACCTATATTGACCTTATACATAATATACATAATTTTATTTATGTATTAATGTTAACATT
17675382 AAC
66 AAC
17675385 TATATATACCTATATTGACCTTATACATAATATACATAATTTTATTTATGTATTAATGTTAACAT
1 TATAT-TACCTATATTGACCTTATACATAATATACATAATTTTATTTATGTATTAATGTTAACAT
17675450 TAAC
65 TAAC
17675454 TAT
1 TAT
17675457 TAGTTAATGT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 5 0.07
69 64 0.93
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (68 bp):
TATATTACCTATATTGACCTTATACATAATATACATAATTTTATTTATGTATTAATGTTAACATT
AAC
Found at i:17697616 original size:19 final size:21
Alignment explanation
Indices: 17697592--17697632 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
17697582 CCATCCTAGT
17697592 ACTATATA-AGTAA-ATATTA
1 ACTATATATAGTAATATATTA
17697611 ACTATATATAGTAATATATTA
1 ACTATATATAGTAATATATTA
17697632 A
1 A
17697633 TACACAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 5 0.25
21 7 0.35
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (21 bp):
ACTATATATAGTAATATATTA
Found at i:17697780 original size:39 final size:39
Alignment explanation
Indices: 17697732--17697810 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
17697722 TAAATATTAA
17697732 AACAATATATATTGTTTATAGTTATAAATTATATAATAT
1 AACAATATATATTGTTTATAGTTATAAATTATATAATAT
*
17697771 AACAGTATATATTGTTTATAGTTATAAATTATATAATAT
1 AACAATATATATTGTTTATAGTTATAAATTATATAATAT
17697810 A
1 A
17697811 TATCTTAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (39 bp):
AACAATATATATTGTTTATAGTTATAAATTATATAATAT
Found at i:17699227 original size:42 final size:42
Alignment explanation
Indices: 17699155--17699354 Score: 188
Period size: 42 Copynumber: 4.8 Consensus size: 42
17699145 GTTGTGTAAT
* * * *
17699155 GATATTGACCGGGCTATGTGCGAGTAGGAGTGCCCATAAGCC
1 GATACTGACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCC
* * * *
17699197 GATACTAACCCGGCTATGTGTGAGTGGGAGTGTGCATAAGCA
1 GATACTGACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCC
* * * *
17699239 AATGCTGACCTGGCTATGTGCGAGTGGGAGTGTGC-TAAGCC
1 GATACTGACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCC
* * * * *
17699280 GATGCTGACCAGACTGTGTGCGAGTAGGAGTGCGCATAAGCC
1 GATACTGACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCC
* * **
17699322 GATGA-TGACCCAGCCATGTGTTAGTGGGAGTGC
1 GAT-ACTGACCCGGCTATGTGCGAGTGGGAGTGC
17699355 ATATGAGTTG
Statistics
Matches: 127, Mismatches: 29, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
41 34 0.27
42 93 0.73
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.23
Consensus pattern (42 bp):
GATACTGACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCC
Found at i:17699331 original size:83 final size:84
Alignment explanation
Indices: 17699160--17699331 Score: 202
Period size: 83 Copynumber: 2.1 Consensus size: 84
17699150 GTAATGATAT
* * * *
17699160 TGACCGGGCTATGTGCGAGTAGGAGTGCCCATAAGCCGATACTAACCCGGCTATGTGTGAGTGGG
1 TGACCGGGCTATGTGCGAGTAGGAGTGCCCATAAGCCGATACTAACCAGACTATGTGCGAGTAGG
* *
17699225 AGTGTGCATAAGCAAATGC
66 AGTGCGCATAAGCAAATGA
* * ** * * *
17699244 TGACCTGGCTATGTGCGAGTGGGAGTGTGC-TAAGCCGATGCTGACCAGACTGTGTGCGAGTAGG
1 TGACCGGGCTATGTGCGAGTAGGAGTGCCCATAAGCCGATACTAACCAGACTATGTGCGAGTAGG
**
17699308 AGTGCGCATAAGCCGATGA
66 AGTGCGCATAAGCAAATGA
17699327 TGACC
1 TGACC
17699332 CAGCCATGTG
Statistics
Matches: 73, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
83 47 0.64
84 26 0.36
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.22
Consensus pattern (84 bp):
TGACCGGGCTATGTGCGAGTAGGAGTGCCCATAAGCCGATACTAACCAGACTATGTGCGAGTAGG
AGTGCGCATAAGCAAATGA
Found at i:17699341 original size:83 final size:84
Alignment explanation
Indices: 17699170--17699354 Score: 192
Period size: 83 Copynumber: 2.2 Consensus size: 84
17699160 TGACCGGGCT
* * * * * *
17699170 ATGTGCGAGTAGGAGTGCCCATAAGCCGATACTAACCCGGCTATGTGTGAGTGGGAGTGTGCATA
1 ATGTGCGAGTGGGAGTGCCCATAAGCCGATACTAACCAGACTATGTGCGAGTAGGAGTGCGCATA
* ** *
17699235 AGCAAATGCTGACCTGGCT
66 AGCAAATGATGACCCAGCC
** * * *
17699254 ATGTGCGAGTGGGAGTGTGC-TAAGCCGATGCTGACCAGACTGTGTGCGAGTAGGAGTGCGCATA
1 ATGTGCGAGTGGGAGTGCCCATAAGCCGATACTAACCAGACTATGTGCGAGTAGGAGTGCGCATA
**
17699318 AGCCGATGATGACCCAGCC
66 AGCAAATGATGACCCAGCC
**
17699337 ATGTGTTAGTGGGAGTGC
1 ATGTGCGAGTGGGAGTGC
17699355 ATATGAGTTG
Statistics
Matches: 81, Mismatches: 20, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
83 64 0.79
84 17 0.21
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.22
Consensus pattern (84 bp):
ATGTGCGAGTGGGAGTGCCCATAAGCCGATACTAACCAGACTATGTGCGAGTAGGAGTGCGCATA
AGCAAATGATGACCCAGCC
Found at i:17699402 original size:2 final size:2
Alignment explanation
Indices: 17699395--17699436 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
17699385 ATGATGATTG
17699395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17699437 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17705874 original size:22 final size:23
Alignment explanation
Indices: 17705838--17705895 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
17705828 TATAGTTTGA
17705838 TTGTTGTAACTTAATT-TGGGCTGT
1 TTGTT-TAA-TTAATTATGGGCTGT
* *
17705862 TTGTTTAATTAATTATGTGTTGT
1 TTGTTTAATTAATTATGGGCTGT
17705885 TT-TTTAATTAA
1 TTGTTTAATTAA
17705896 AATTTGAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 15 0.48
23 11 0.35
24 5 0.16
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.57
Consensus pattern (23 bp):
TTGTTTAATTAATTATGGGCTGT
Found at i:17717999 original size:13 final size:13
Alignment explanation
Indices: 17717981--17718005 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17717971 AGAGAAATTG
17717981 TGATTTTATAAAA
1 TGATTTTATAAAA
17717994 TGATTTTATAAA
1 TGATTTTATAAA
17718006 TTTTTTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:17725339 original size:28 final size:27
Alignment explanation
Indices: 17725293--17725345 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
17725283 GTGTTCTGGT
** *
17725293 GGTGGAAAATTACTGTTTTGCCCTTGG
1 GGTGGAAAATTACCATTTTACCCTTGG
17725320 GGTGGTAAAATTACCATTTTACCCTT
1 GGTGG-AAAATTACCATTTTACCCTT
17725346 ATACTTCGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (27 bp):
GGTGGAAAATTACCATTTTACCCTTGG
Found at i:17742404 original size:20 final size:21
Alignment explanation
Indices: 17742379--17742424 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
17742369 ATATTTTCTG
*
17742379 TTTTTCAT-TTACCT-AATCTA
1 TTTTTCATATTA-CTAAATATA
17742399 TTTTTCATATTACTAAATATA
1 TTTTTCATATTACTAAATATA
17742420 TTTTT
1 TTTTT
17742425 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTCATATTACTAAATATA
Found at i:17743455 original size:16 final size:15
Alignment explanation
Indices: 17743436--17743469 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
17743426 TGTCTTTCCA
17743436 TTTTTTCTCCTTTTCTT
1 TTTTTTC-CCTTTT-TT
17743453 TTTTTTCCCTTTTTT
1 TTTTTTCCCTTTTTT
17743468 TT
1 TT
17743470 ATAAGAGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 6 0.35
17 7 0.41
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTCCCTTTTTT
Found at i:17743924 original size:20 final size:21
Alignment explanation
Indices: 17743901--17743951 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 21
17743891 ACCCATAATA
17743901 AAAAATAAATGCAAAT-AAAC
1 AAAAATAAATGCAAATAAAAC
*
17743921 AAAAATAAATGCAAATAGAAAT
1 AAAAATAAATGCAAATA-AAAC
17743943 AAAAATAAA
1 AAAAATAAA
17743952 ATTGAATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 16 0.57
22 12 0.43
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.16
Consensus pattern (21 bp):
AAAAATAAATGCAAATAAAAC
Found at i:17744222 original size:29 final size:29
Alignment explanation
Indices: 17744189--17744248 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
17744179 CCAAGAATGG
17744189 TCAAGTCCATTCTTTATATAGGTTGATAC
1 TCAAGTCCATTCTTTATATAGGTTGATAC
17744218 TCAAGTCCATTCTTTATATAGGTTGATAC
1 TCAAGTCCATTCTTTATATAGGTTGATAC
17744247 TC
1 TC
17744249 TAGTAGCCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (29 bp):
TCAAGTCCATTCTTTATATAGGTTGATAC
Found at i:17761291 original size:3 final size:3
Alignment explanation
Indices: 17761283--17761329 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
17761273 ATATAGTTAT
*
17761283 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAT TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
17761330 GAGATAAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (3 bp):
TAC
Found at i:17762846 original size:8 final size:8
Alignment explanation
Indices: 17762828--17762920 Score: 73
Period size: 8 Copynumber: 11.8 Consensus size: 8
17762818 AAGTTTTTGT
17762828 TGGGT-AA
1 TGGGTAAA
17762835 TGGGTAAA
1 TGGGTAAA
* *
17762843 TGGGTTAG
1 TGGGTAAA
* *
17762851 TGAGTAAG
1 TGGGTAAA
*
17762859 TAGGTAAA
1 TGGGTAAA
*
17762867 TGGGTAATN
1 TGGGTAA-A
* *
17762876 TGGGTTAG
1 TGGGTAAA
*
17762884 TGGGTAAG
1 TGGGTAAA
17762892 TGGGTAAA
1 TGGGTAAA
*
17762900 TGGGTAAT
1 TGGGTAAA
17762908 TGGGT-AA
1 TGGGTAAA
17762915 TGGGTA
1 TGGGTA
17762921 GTCCAAATGA
Statistics
Matches: 68, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
7 11 0.16
8 51 0.75
9 6 0.09
ACGTcount: A:0.28, C:0.00, G:0.41, T:0.30
Consensus pattern (8 bp):
TGGGTAAA
Found at i:17762873 original size:16 final size:16
Alignment explanation
Indices: 17762828--17762920 Score: 82
Period size: 16 Copynumber: 5.9 Consensus size: 16
17762818 AAGTTTTTGT
*
17762828 TGGGT-AATGGGTAAA
1 TGGGTAAATGGGTAAG
* * *
17762843 TGGGTTAGTGAGTAAG
1 TGGGTAAATGGGTAAG
* *
17762859 TAGGTAAATGGGTAATN
1 TGGGTAAATGGGTAA-G
* *
17762876 TGGGTTAGTGGGTAAG
1 TGGGTAAATGGGTAAG
*
17762892 TGGGTAAATGGGTAAT
1 TGGGTAAATGGGTAAG
17762908 TGGGT-AATGGGTA
1 TGGGTAAATGGGTA
17762921 GTCCAAATGA
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
15 13 0.21
16 36 0.59
17 12 0.20
ACGTcount: A:0.28, C:0.00, G:0.41, T:0.30
Consensus pattern (16 bp):
TGGGTAAATGGGTAAG
Found at i:17762884 original size:33 final size:32
Alignment explanation
Indices: 17762833--17762912 Score: 124
Period size: 33 Copynumber: 2.5 Consensus size: 32
17762823 TTTGTTGGGT
*
17762833 AATGGGTAAATGGGTTAGTGAGTAAGTAGGTA
1 AATGGGTAATTGGGTTAGTGAGTAAGTAGGTA
* *
17762865 AATGGGTAATNTGGGTTAGTGGGTAAGTGGGTA
1 AATGGGTAAT-TGGGTTAGTGAGTAAGTAGGTA
17762898 AATGGGTAATTGGGT
1 AATGGGTAATTGGGT
17762913 AATGGGTAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 14 0.32
33 30 0.68
ACGTcount: A:0.29, C:0.00, G:0.40, T:0.30
Consensus pattern (32 bp):
AATGGGTAATTGGGTTAGTGAGTAAGTAGGTA
Found at i:17764608 original size:21 final size:21
Alignment explanation
Indices: 17764556--17764623 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
17764546 TTGAATGGAG
* * *
17764556 GCATCAGTCCTTATCATAAAT
1 GCATCAGTCTTTGTCATGAAT
* *
17764577 GCATCAATCTTTGTTATGAAT
1 GCATCAGTCTTTGTCATGAAT
17764598 GCATCAGTCTTTGTCATGAATT
1 GCATCAGTCTTTGTCATGAA-T
17764620 GCAT
1 GCAT
17764624 GAACATATCC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 34 0.87
22 5 0.13
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (21 bp):
GCATCAGTCTTTGTCATGAAT
Found at i:17766539 original size:13 final size:13
Alignment explanation
Indices: 17766521--17766545 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17766511 TTCTAGAAAA
17766521 TTTATAAAATCAT
1 TTTATAAAATCAT
17766534 TTTATAAAATCA
1 TTTATAAAATCA
17766546 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:17769785 original size:26 final size:26
Alignment explanation
Indices: 17769749--17769803 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
17769739 GTTTCCAACT
17769749 CAATCTAATTGGTGATCAGGCAATTA
1 CAATCTAATTGGTGATCAGGCAATTA
17769775 CAATCTAATTGGTGATCAGGCAATTA
1 CAATCTAATTGGTGATCAGGCAATTA
17769801 CAA
1 CAA
17769804 GCATTAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (26 bp):
CAATCTAATTGGTGATCAGGCAATTA
Found at i:17771564 original size:14 final size:14
Alignment explanation
Indices: 17771535--17771573 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
17771525 ATTTAGAATC
17771535 AATAATTAT-A-AA
1 AATAATTATAACAA
17771547 AATAATTATAACAA
1 AATAATTATAACAA
*
17771561 AATAATAATAACA
1 AATAATTATAACA
17771574 TCAAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 9 0.38
13 1 0.04
14 14 0.58
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAATTATAACAA
Found at i:17775427 original size:19 final size:19
Alignment explanation
Indices: 17775403--17775439 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
17775393 CTTCTAAACT
17775403 TCAAATCATACTCCAATAC
1 TCAAATCATACTCCAATAC
17775422 TCAAATCATACTCCAATA
1 TCAAATCATACTCCAATA
17775440 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (19 bp):
TCAAATCATACTCCAATAC
Found at i:17776595 original size:40 final size:40
Alignment explanation
Indices: 17776539--17776635 Score: 169
Period size: 40 Copynumber: 2.4 Consensus size: 40
17776529 CATATATTAA
*
17776539 GACAGTTTGACATATATAATAAGAAACACTAAAAGGGCTT
1 GACAGTTTGACCTATATAATAAGAAACACTAAAAGGGCTT
17776579 GACAGTTTGACCTATATAATAAGAAACACTAAAAGGGCTT
1 GACAGTTTGACCTATATAATAAGAAACACTAAAAGGGCTT
17776619 GACAGTTTG-CCTTATAT
1 GACAGTTTGACC-TATAT
17776636 TGGGACTTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
39 2 0.04
40 53 0.96
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (40 bp):
GACAGTTTGACCTATATAATAAGAAACACTAAAAGGGCTT
Found at i:17777121 original size:26 final size:26
Alignment explanation
Indices: 17777092--17777144 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
17777082 CCTCTCATAT
* *
17777092 AAAATCTTGAATTTATCGTTGTTCTA
1 AAAATCTTGAATTCATCATTGTTCTA
17777118 AAAATCTTGAATTCATCATTGTTCTA
1 AAAATCTTGAATTCATCATTGTTCTA
17777144 A
1 A
17777145 GATAACCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (26 bp):
AAAATCTTGAATTCATCATTGTTCTA
Found at i:17777659 original size:27 final size:27
Alignment explanation
Indices: 17777614--17777665 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
17777604 TATTCAACAG
*
17777614 AAAAAAATATCAATTTAA-TAAAATAT
1 AAAAAAATATCAAATTAATTAAAATAT
*
17777640 AAAACAATATTCAAATTAATTAAAAT
1 AAAAAAATA-TCAAATTAATTAAAAT
17777666 TTCAAATACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 8 0.36
28 6 0.27
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (27 bp):
AAAAAAATATCAAATTAATTAAAATAT
Found at i:17778453 original size:21 final size:20
Alignment explanation
Indices: 17778417--17778458 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
17778407 GTGAACATTG
*
17778417 AAAAGGGGGAATAGGAAAAA
1 AAAAGGGGGAAGAGGAAAAA
17778437 AAAAGGGGGAAAGAGGAGAAAA
1 AAAAGGGGG-AAGAGGA-AAAA
17778459 GCTATTAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 6 0.32
22 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (20 bp):
AAAAGGGGGAAGAGGAAAAA
Found at i:17782155 original size:2 final size:2
Alignment explanation
Indices: 17782148--17782194 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
17782138 GCAGTTAACC
*
17782148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17782190 AT AT A
1 AT AT A
17782195 CTAAAAGAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.